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<p>Hi Francesco</p>
<p>We have just pushed a fix to the MySQLTransfer.pm runnable, so
that it no longer locks tables by default. If you go to your eHive
checkout and perform a git pull, you should get this fix. <br>
</p>
<p>Users who wish to retain the table locking behavior can switch it
on by passing a parameter 'lock_tables=1' to MySQLTransfer.pm</p>
<p>Best<br>
-Brandon<br>
</p>
<br>
<div class="moz-cite-prefix">On 09/11/2017 16:20, Mateus Patricio
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:E7B1981D-D367-495C-8AFB-2DF9A4F86624@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<div class="">Hi Francesco,</div>
<div class=""><br class="">
</div>
<div class="">So what’s happening here is that you are trying to
lock a table in one of our servers.</div>
<div class=""><br class="">
</div>
<div class="">That can be fixed by telling mysqldump to avoid
locking the table. (Like you initially suspected)</div>
<div class=""><br class="">
</div>
<div class="">You could do that directly on the eHive runnable
"ehive/master/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm”</div>
<div class=""><br class="">
</div>
<div class="">The dump command is constructed at:</div>
<div class=""><a
href="https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117"
class="" moz-do-not-send="true">https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117</a></div>
<div class=""><br class="">
</div>
<div class="">I would suggest you to create a new entry to
“mode_options”:</div>
<div class=""><a
href="https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112"
class="" moz-do-not-send="true">https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112</a></div>
<div class=""><br class="">
</div>
<div class="">So that you could access directly from your pipeline
config file, by setting something like:</div>
<div class="">
<div class=""><br class="">
</div>
</div>
<blockquote type="cite" class="">
<div class="">
<div class=""><font class="" face="Courier New"> {
-logic_name => 'copy_ncbi_table',</font></div>
<div class=""><font class="" face="Courier New">
-module =>
'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer',</font></div>
<div class=""><font class="" face="Courier New">
-parameters => {</font></div>
<div class=""><font class="" face="Courier New">
'src_db_conn' => '#ncbi_db#',</font></div>
<div class=""><font class="" face="Courier New">
'mode' => ’<b class="">SKIP_LOCK</b>',</font></div>
<div class=""><font class="" face="Courier New">
'filter_cmd' => 'sed
"s/ENGINE=MyISAM/ENGINE=InnoDB/"',</font></div>
<div class=""><font class="" face="Courier New"> },</font></div>
<div class=""><font class="" face="Courier New"> },</font></div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Please let me know if that doesn’t work.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
</div>
<div class="">Mateus.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class=""><br class="">
</div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 9 Nov 2017, at 15:44, Francesco Lamanna
<<a href="mailto:francesco.lamanna@gmail.com" class=""
moz-do-not-send="true">francesco.lamanna@gmail.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">Hi Mateus,<br class="">
<br class="">
</div>
thank you for your answer.<br class="">
<br class="">
</div>
I am using 'ncbi_db' => 'mysql://<a
href="http://anonymous@ensembldb.ensembl.org/ensembl_compara_90"
class="" moz-do-not-send="true">anonymous@ensembldb.ensembl.org/ensembl_compara_90</a>'
to conncect to ncbi_db (I used the same value as
in the NoMasterProteinTrees_conf.pm example).<br
class="">
<br class="">
</div>
The failing analysis is copy_ncbi_table(9).<br
class="">
<br class="">
</div>
Cheers,<br class="">
</div>
Francesco.<br class="">
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">2017-11-09 16:29 GMT+01:00
Mateus Patricio <span dir="ltr" class=""><<a
href="mailto:mateus@ebi.ac.uk" target="_blank"
class="" moz-do-not-send="true">mateus@ebi.ac.uk</a>></span>:<br
class="">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Hi
Francesco,
<div class=""><br class="">
</div>
<div class="">Looks like your pipeline is using
the user anonymous to connect to the database.</div>
<div class=""><br class="">
</div>
<div class="">I would suggest that you add the
skip option within your runnable.</div>
<div class=""><br class="">
</div>
<div class="">Which analysis is actually failing?</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
</div>
<div class="">Mateus.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">
<div class="h5">
<div class="">On 8 Nov 2017, at 17:36,
Francesco Lamanna <<a
href="mailto:francesco.lamanna@gmail.com"
target="_blank" class=""
moz-do-not-send="true">francesco.lamanna@gmail.com</a>>
wrote:</div>
<br
class="m_-3216016505973850452Apple-interchange-newline">
</div>
</div>
<div class="">
<div class="">
<div class="h5">
<div dir="ltr" class="">
<div class="">
<div class="">
<div class="">
<div class="">Hello,<br
class="">
<br class="">
</div>
I am trying to apply the
ProteinTrees pipeline to a set
of Ensembl and non-Ensembl
genomes. <br class="">
<br class="">
When running the pipeline
without a master database (via
<a href="http://beekeeper.pl/"
target="_blank" class=""
moz-do-not-send="true">beekeeper.pl</a>)
I get the following error:<br
class="">
<br class="">
ensembl_compara_90
ncbi_taxa_node | sed
"s/ENGINE=MyISAM/ENGINE=<wbr
class="">InnoDB/" | mysql
-h127.0.0.1 -P3306 -uroot
-p$EHIVE_TMP_PASSWORD_0
hd_cc141_test_protein_trees_<wbr
class="">no_master_90'
resulted in an error code=2<br
class="">
stderr is: mysql: [Warning]
Using a password on the
command line interface can be
insecure.<br class="">
mysqldump: Got error: 1044:
Access denied for user
'anonymous'@'%' to database
'ensembl_compara_90' when
doing LOCK TABLES <br
class="">
<br class="">
<br class="">
</div>
Is there a way to pass
--skip-lock-tables to the
pipeline (e.g. in the conf file)
in order to be able to dump the
database?<br class="">
<br class="">
</div>
Thanks,<br class="">
</div>
Francesco.<br class="">
<div class="">
<div class="">
<div class=""><br class="">
<br class="">
</div>
</div>
</div>
</div>
</div>
</div>
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</div>
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